Research workbench
Crystal structure of beta-D-xylosidase from dictyoglomus thermophilum in ligand-free form
Analyse Crystal structure of beta-D-xylosidase from dictyoglomus thermophilum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YYH
- Type
- protein
- Length
- 1,002 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- EC
- 3.2.1.37
- UniProt
- B5YB78
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-xylosidase (EC 3.2.1.37) | protein | 502 | 33% helix, 26% strand | B5YB78 |
| B | Beta-xylosidase (EC 3.2.1.37) | protein | 500 | 32% helix, 27% strand | B5YB78 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CIT · Citric acid · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.76 | 0.78 | 147 | CIT, EDO |
| 2 | 214 | 0.62 | 0.82 | 34 | empty |
| 3 | 200 | 0.61 | 0.82 | 34 | empty |
| 4 | 217 | 0.53 | 0.77 | 31 | empty |
| 5 | 153 | 0.43 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1651 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6YYH · Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum in ligand-free form · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B5YB78
- Elsewhere: RCSB PDB 6YYH · PDBe 6YYH · UniProt B5YB78
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